BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716504.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,828,423 number of mapped reads = 2,491,659 (88.09%) number of supplementary alignments = 9,984 (0.35%) number of secondary alignments = 0 number of mapped bases = 142,154,040 bp number of sequenced bases = 142,110,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,272 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8918 >>>>>>> ACTG content number of A's = 34,919,451 bp (24.57%) number of C's = 28,190,497 bp (19.84%) number of T's = 46,320,458 bp (32.59%) number of G's = 32,679,205 bp (23%) number of N's = 1,034 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 755,259 number of insertions = 9,424 mapped reads with insertion percentage = 0.38% number of deletions = 27,180 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.41% >>>>>>> Coverage mean coverageData = 0.0459X std coverageData = 0.3611X There is a 3.9% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11367276 0.04560580813959136 0.4803496686504487 chr2 243199373 11856848 0.04875361253501258 0.6159505788568396 chr3 198022430 9430997 0.047625902782831214 0.2561137389559408 chr4 191154276 9099983 0.04760543781924083 0.29594140800174606 chr5 180915260 8483003 0.04688937240562239 0.24997963612681703 chr6 171115067 8110927 0.04740042558613497 0.3014370855504373 chr7 159138663 7890765 0.049584210720684516 0.4342214375960916 chr8 146364022 7002812 0.047845173317251424 0.3584605367561256 chr9 141213431 5919863 0.04192138777507644 0.2952041447274358 chr10 135534747 6789693 0.050095589140694674 0.44928462597310476 chr11 135006516 6317814 0.0467963635177431 0.3136583583944693 chr12 133851895 6451036 0.0481953281274053 0.25783735871334307 chr13 115169878 4431106 0.038474521957902914 0.2256666098681508 chr14 107349540 4275869 0.03983127454481873 0.24250013867748252 chr15 102531392 4172336 0.0406932542181813 0.23744933589585923 chr16 90354753 4305867 0.04765512446257254 0.2843903022482595 chr17 81195210 4010508 0.04939340633517667 0.27067866068760443 chr18 78077248 3739599 0.04789614254846687 0.4489793612811097 chr19 59128983 3147452 0.053230274567719185 0.4280905038429521 chr20 63025520 3051172 0.04841169101024474 0.2696363042699063 chr21 48129895 1843507 0.038302743024891284 0.26059699030020245 chr22 51304566 1749148 0.03409341772816088 0.2150512066033112 chrMT 16571 154722 9.336913885703941 6.039131696034855 chrX 155270560 8084661 0.05206821563598405 0.29314604158191915 chrY 59373566 467076 0.007866733151921513 0.22894474983579957